Examples:

The Clans in K never refer to their powers as magic. The Slate is an "energy source". Their powers aren't from any standard, they don't all operate the same way, and they're quite easy to lose control of, but "magic" is never used. It's possible that they're trying to avoid the dreamy, inspiring connotations of "magic", since their powers are something frightening, with intense potential for disaster. The Green Clan's more versatile powers (incl. walking through walls) are frequently called a "manipulation ability", a particularly standout example of this.

The lines between esper abilities and magic are further broken down when it turns out that that the training programme for unlocking esper potential was invented by a mage, based on a ritual intended to give the user traits of angels (and that the so-far theoretical Level 6 espers are essentially Deities of Human Origin). And while most esper powers are based on a clear scientific concept, such as control over electricity or friction, the Gemstones (espers who unlocked their powers at a young age without training) often have far more abstract powers or ones that seem to do multiple unrelated things.

Fushigiboshi No Futago Hime: The Prominence and the Power of Darkness. Neither are explicitly called magic despite looking just like it. Altezza refers to the former as Fine and Rein's "weird power".

Comic Books

In the Valiant Comics titles set in the 41st Century (Magnus: Robot Fighter, Rai and the Future Force and Psi-Lords), "ectotheric energy" is used by some people to achieve the effect of "magic", even though it is in reality a variation of Psychic Powers and is scientifically comprehensible. "Necromancy" occurs in many titles from the 20th Century, and is even more overtly expressed as a kind of "magic" (obviously, given the name), although it too is really psychic in nature.

In Opening Dangerous Gates, Kisuke Urahara tells the Fairy Tail characters that magic and reiatsu are one and the same. Every one has a reserve of energy in their bodies, but only some people can access it, and it has different effects based on the individual and how they apply it.

In The Matrix, bending the rules of physics while jacked into the computer world is ostensibly just hacking a program, but tends to be accorded mystical significance. Then Neo starts controlling machines in the real world with his mind alone....

The Wheel of Time: The One Power, which is segregated by sex, with males using saidin and females saidar. Using the Power is called channeling. The Big Bad has his own flavor, called the True Power. Then there are miscellaneous bits of Outside Context Magic floating around, like dudes who can talk to wolves, Ogier Treesinging, Dreamwalking, and Min's aura vision. All of it is clearly magical, but the word "magic" is never used; the closest they come is when Aes Sedai (female users of the One Power) are occasionally called "witches" as a pejorative.

Brandon Sanderson's "cosmere" multiverse in general uses this; individual systems of Functional Magic are referred to by their names, and the term "magic" hardly ever comes up. The exception is in The Stormlight Archive, where one magic system is called "the Old Magic". In The Alloy of Law, allomancy is referred to as magic a few times. By contrast, the multiverse's resident Meta Guy, in the appendix of the same book, seems to refer to all forms of magic as "investiture", but exactly what this means is not yet explained.

The King Killer Chronicle: Sympathy, not to be confused with "Naming". If you know the true name of something you can command it, but if you don't then you can find something to represent it and use your willpower to force what happens to this to happen to that. Sympathy is seen as magic by many people in-universe, but people who actually use it insist that it isn't.

Strength & Justice firmly assures that everyone's powers in the books are called "dynas" (short for "dynamism"), but at several points magic circles are said to appear when a dyna is in use, and the history of the city very clearly states that the users are all with an innate magical capability. It's a bit unclear as to what it is exactly.

The Chronicles of Thomas Covenant has Earthpower, an ambient quasi-mystical energy of The Land, which some humans can channel to devastating effect. Though the series also has magic (via the Wild Magic of white gold [platinum]). Comparably, Earthpower is fire, wild magic is an atom bomb.

Live-Action TV

In Star Trek, humans are absolutely militant about this. No matter how scientifically-inexplicable something is, or if that something can outright change the laws of physics at will, it is still not "magic". Referring to it as such will provoke an immediate negative response and denial. Technobabble, even if it is completely unsupported by evidence, will invariably be accepted as an explanation before "magic" will. Things which would be considered "supernatural" in real life such as Psychic Powers or Reality Warpers are still regarded as scientific in nature, even though Federation science cannot explain them. Which is why talking about the limitless power of "thought" is acceptable, but using the m-word will get you an earful of Flat Earth Atheism.

The Carrionites — witches who used what the Doctor insisted was not magic, but physics based on words rather than numbers.

It also has Block Transfer Computations — complex mathematical equations that were never openly compared to magic, but the most blatant use of them (at least until the novels decided that TARDISes were made out of them) involved a planet of monastic aliens chanting arcane formulae to reshape reality.

A funny lampshade (or is it a reference) is made in the Tenth Doctor's episode "The Girl in the Fireplace", where he says that the window they're looking through to XVIII century France is a "spatial-temporal hyperlink".

Rose: What's that mean? The Doctor: No idea, I just made it up. Didn't want to say "magic door".

Tabletop Games

Warhammer 40,000: The Warp and psionics, but Chaotic practitioners don't shy from calling themselves wizards. As a comparison, in the Warhammer universe — as befitting fantasy — the Warp is unashamedly magic.

In Nomine: Songs and Sorcery, one of the rulebooks notes that many of those in the know will get annoyed with anybody calling Songs "magic", and some will also get annoyed about using that term for Sorcery. Also you don't "cast" Songs, you perform them.

Psionics in Dungeons & Dragons can fall somewhere in or near this trope depending on the edition and variant rules. The default in arguably the most popular incarnation is "magic/psionics transparency", where spells and psionic powers are identical (i.e. Dispel Magic works on psionics and vice versa) and in some settings psionics is outright referred to as a type of magic. The main difference between the two is that spellcasters work with external energy using predefined spells as templates (giving them larger numbers of techniques), while psions work with internal energy which they shape directly through willpower (making their individual techniques more flexible). Earlier editions and mentioned variant rules, however, make psionics fully or partly disconnected from magic (i.e. Dispel Magic does not work on psionics and vice versa), while still having the same magic-like techniques.

The Lord of the Rings Online: Rune-Keepers and Lore-Masters, to get around the fact that there are canonically only five wizards in all of Middle-Earth.note Gandalf, Saruman, Radagast, Alatar and Pallando.

Mass Effect: Biotics. It's basically telekinesis and kinetic energy bolts by another name - extremely detailed justifications, but in the end, its still lift spells. All of the advanced technology in the setting works off the same principles.

Phantasy Star: It's an ostensibly Space Opera and Planetary Romance, but ESP and "techniques" are functionally magic, with true magic being generally considered to be a rare lost art which only a select few can wield.

StarCraft: Psionics (Complete with glowing hands in the sequel even though it is supposed to be a mental power.)

Star Ocean: Heraldry, Symbology, Runeology, Whateverology... Justified in-universe as being programming code—the universe is actually an MMORPG, and magic is really just the AI hacking the system, and the eponymous symbols and runes are the game's code.

Xenogears, Xenosaga, and Xenoblade: Ether. At least in the case of Xenosaga, a lot of this is explicitly stated to be nanobots in the environs being somehow influenced by the characters. The effects are still just like magic.

The Matrix Online: Hacking. Building on the Matrix films' exploration of Magic from Technology, the game introduces an entire character class built around casting spells by hacking into the Matrix's code from within. Every "spell" is accompanied by an explosion of green binary code, just to remind players that it's not really magic.

In the Shinobi series, "ninjutsu" is the name generally used to describe special magical attacks based on fire, lightning, etc.

RWBY: Subverted. Word of God states that Dust was used in place of magic to intentionally avoid using the word during their RTX panel. However, since then, he, and the rest of the staff, have freely described certain characters as "mages". And as it turns out, there are literal magic users in this world whose powers are not related to Dust or Aura. And one of them happens to be the Big Bad...

The Spark. Semi-example. The machines are powered by science, but you have to be born with the mysterious "spark" to make them work, and once you do, you can kind of bend the laws of physics. It's not clear to what extent, though, since the technology is never clearly explained.

The old stories and legends of the setting's current Steam Punk era include magic-using figures (explicitly as ancestors to the "modern" scientists), hinting that the Spark may indeed be some kind of Reality Warper power which manifests through the individual's understanding of how the world works (i.e. people used to believe in magic, so Sparks did magic, science has replaced that worldview, so Sparks do science).

Before the main plot kicks off and keeps him busy, the Baron used his (very limited) free time working on a side project where he was actually experimenting on the brains of Sparks (namely those who were too dangerous to let live anyway) to try to determine the origin of the phenomenon.

The Story of Anima, Anima is a mysterious force emitted by all individuals. Its exact nature is unknown; in fact, it's only called Anima because the theory that it's Soul Power is the most popular one. While normally it can only be wielded through the aid of Catalysts, some people, known as Animus, are capable of harnessing their own Anima into unique super powers.

Web Original

At no point in Funny Business are Jeannette's Reality Warper powers called magic, even though that's what most people the characters' ages would think to call the ability to ignore the laws of physics at will. They're generically called her "abilities" or "powers" instead.

The debate between magic-users and scientists in the Whateley Universe whether magic is just "psychic powers" or whether psychics in turn are just this trope keeps going. In the meantime, a new approach called "pattern theory" offers potential insight into where superpowers in the setting come from in general, but is still very much in its embryonic stage as well as apparently nigh incomprehensible to most people.

Prolecto has the abilities of angels, demons, and members of certain sects of the Survivalist Project. Like Kayla.

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